src/gromacs/mdlib/force.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
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  19  * Lesser General Public License for more details.
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  36  */
  37 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include <assert.h>
  42 #include <math.h>
  43 #include <string.h>
  44
  45 #include "typedefs.h"
  46 #include "macros.h"
  47 #include "macros.h"
  48 #include "physics.h"
  49 #include "force.h"
  50 #include "nonbonded.h"
  51 #include "names.h"
  52 #include "network.h"
  53 #include "pbc.h"
  54 #include "ns.h"
  55 #include "nrnb.h"
  56 #include "bondf.h"
  57 #include "mshift.h"
  58 #include "txtdump.h"
  59 #include "coulomb.h"
  60 #include "pme.h"
  61 #include "mdrun.h"
  62 #include "domdec.h"
  63 #include "qmmm.h"
  64 #include "gmx_omp_nthreads.h"
  65
  66 #include "gromacs/legacyheaders/types/commrec.h"
  67 #include "gromacs/math/vec.h"
  68 #include "gromacs/timing/wallcycle.h"
  69 #include "gromacs/utility/fatalerror.h"
  70 #include "gromacs/utility/smalloc.h"
  71
  72 void ns(FILE              *fp,
  73         t_forcerec        *fr,
  74         matrix             box,
  75         gmx_groups_t      *groups,
  76         gmx_localtop_t    *top,
  77         t_mdatoms         *md,
  78         t_commrec         *cr,
  79         t_nrnb            *nrnb,
  80         gmx_bool           bFillGrid,
  81         gmx_bool           bDoLongRangeNS)
  82 {
  83     char   *ptr;
  84     int     nsearch;
  85
  86
  87     if (!fr->ns.nblist_initialized)
  88     {
  89         init_neighbor_list(fp, fr, md->homenr);
  90     }
  91
  92     if (fr->bTwinRange)
  93     {
  94         fr->nlr = 0;
  95     }
  96
  97     nsearch = search_neighbours(fp, fr, box, top, groups, cr, nrnb, md,
  98                                 bFillGrid, bDoLongRangeNS);
  99     if (debug)
 100     {
 101         fprintf(debug, "nsearch = %d\n", nsearch);
 102     }
 103
 104     /* Check whether we have to do dynamic load balancing */
 105     /*if ((nsb->nstDlb > 0) && (mod(step,nsb->nstDlb) == 0))
 106        count_nb(cr,nsb,&(top->blocks[ebCGS]),nns,fr->nlr,
 107        &(top->idef),opts->ngener);
 108      */
 109     if (fr->ns.dump_nl > 0)
 110     {
 111         dump_nblist(fp, cr, fr, fr->ns.dump_nl);
 112     }
 113 }
 114
 115 static void reduce_thread_forces(int n, rvec *f,
 116                                  tensor vir_q, tensor vir_lj,
 117                                  real *Vcorr_q, real *Vcorr_lj,
 118                                  real *dvdl_q, real *dvdl_lj,
 119                                  int nthreads, f_thread_t *f_t)
 120 {
 121     int t, i;
 122
 123     /* This reduction can run over any number of threads */
 124 #pragma omp parallel for num_threads(gmx_omp_nthreads_get(emntBonded)) private(t) schedule(static)
 125     for (i = 0; i < n; i++)
 126     {
 127         for (t = 1; t < nthreads; t++)
 128         {
 129             rvec_inc(f[i], f_t[t].f[i]);
 130         }
 131     }
 132     for (t = 1; t < nthreads; t++)
 133     {
 134         *Vcorr_q  += f_t[t].Vcorr_q;
 135         *Vcorr_lj += f_t[t].Vcorr_lj;
 136         *dvdl_q   += f_t[t].dvdl[efptCOUL];
 137         *dvdl_lj  += f_t[t].dvdl[efptVDW];
 138         m_add(vir_q, f_t[t].vir_q, vir_q);
 139         m_add(vir_lj, f_t[t].vir_lj, vir_lj);
 140     }
 141 }
 142
 143 void gmx_print_sepdvdl(FILE *fplog, const char *s, real v, real dvdlambda)
 144 {
 145     fprintf(fplog, "  %-30s V %12.5e  dVdl %12.5e\n", s, v, dvdlambda);
 146 }
 147
 148 void do_force_lowlevel(FILE       *fplog,   gmx_int64_t step,
 149                        t_forcerec *fr,      t_inputrec *ir,
 150                        t_idef     *idef,    t_commrec  *cr,
 151                        t_nrnb     *nrnb,    gmx_wallcycle_t wcycle,
 152                        t_mdatoms  *md,
 153                        rvec       x[],      history_t  *hist,
 154                        rvec       f[],
 155                        rvec       f_longrange[],
 156                        gmx_enerdata_t *enerd,
 157                        t_fcdata   *fcd,
 158                        gmx_localtop_t *top,
 159                        gmx_genborn_t *born,
 160                        t_atomtypes *atype,
 161                        gmx_bool       bBornRadii,
 162                        matrix     box,
 163                        t_lambda   *fepvals,
 164                        real       *lambda,
 165                        t_graph    *graph,
 166                        t_blocka   *excl,
 167                        rvec       mu_tot[],
 168                        int        flags,
 169                        float      *cycles_pme)
 170 {
 171     int         i, j;
 172     int         donb_flags;
 173     gmx_bool    bDoEpot, bSepDVDL, bSB;
 174     int         pme_flags;
 175     matrix      boxs;
 176     rvec        box_size;
 177     t_pbc       pbc;
 178     char        buf[22];
 179     double      clam_i, vlam_i;
 180     real        dvdl_dum[efptNR], dvdl_nb[efptNR], lam_i[efptNR];
 181     real        dvdl_q, dvdl_lj;
 182
 183 #ifdef GMX_MPI
 184     double  t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
 185 #endif
 186
 187 #define PRINT_SEPDVDL(s, v, dvdlambda) if (bSepDVDL) { gmx_print_sepdvdl(fplog, s, v, dvdlambda); }
 188
 189     set_pbc(&pbc, fr->ePBC, box);
 190
 191     /* reset free energy components */
 192     for (i = 0; i < efptNR; i++)
 193     {
 194         dvdl_nb[i]  = 0;
 195         dvdl_dum[i] = 0;
 196     }
 197
 198     /* Reset box */
 199     for (i = 0; (i < DIM); i++)
 200     {
 201         box_size[i] = box[i][i];
 202     }
 203
 204     bSepDVDL = (fr->bSepDVDL && do_per_step(step, ir->nstlog));
 205     debug_gmx();
 206
 207     /* do QMMM first if requested */
 208     if (fr->bQMMM)
 209     {
 210         enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr);
 211     }
 212
 213     if (bSepDVDL)
 214     {
 215         fprintf(fplog, "Step %s: non-bonded V and dVdl for node %d:\n",
 216                 gmx_step_str(step, buf), cr->nodeid);
 217     }
 218
 219     /* Call the short range functions all in one go. */
 220
 221 #ifdef GMX_MPI
 222     /*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
 223 #define TAKETIME FALSE
 224     if (TAKETIME)
 225     {
 226         MPI_Barrier(cr->mpi_comm_mygroup);
 227         t0 = MPI_Wtime();
 228     }
 229 #endif
 230
 231     if (ir->nwall)
 232     {
 233         /* foreign lambda component for walls */
 234         real dvdl_walls = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
 235                                    enerd->grpp.ener[egLJSR], nrnb);
 236         PRINT_SEPDVDL("Walls", 0.0, dvdl_walls);
 237         enerd->dvdl_lin[efptVDW] += dvdl_walls;
 238     }
 239
 240     /* If doing GB, reset dvda and calculate the Born radii */
 241     if (ir->implicit_solvent)
 242     {
 243         wallcycle_sub_start(wcycle, ewcsNONBONDED);
 244
 245         for (i = 0; i < born->nr; i++)
 246         {
 247             fr->dvda[i] = 0;
 248         }
 249
 250         if (bBornRadii)
 251         {
 252             calc_gb_rad(cr, fr, ir, top, x, &(fr->gblist), born, md, nrnb);
 253         }
 254
 255         wallcycle_sub_stop(wcycle, ewcsNONBONDED);
 256     }
 257
 258     where();
 259     /* We only do non-bonded calculation with group scheme here, the verlet
 260      * calls are done from do_force_cutsVERLET(). */
 261     if (fr->cutoff_scheme == ecutsGROUP && (flags & GMX_FORCE_NONBONDED))
 262     {
 263         donb_flags = 0;
 264         /* Add short-range interactions */
 265         donb_flags |= GMX_NONBONDED_DO_SR;
 266
 267         /* Currently all group scheme kernels always calculate (shift-)forces */
 268         if (flags & GMX_FORCE_FORCES)
 269         {
 270             donb_flags |= GMX_NONBONDED_DO_FORCE;
 271         }
 272         if (flags & GMX_FORCE_VIRIAL)
 273         {
 274             donb_flags |= GMX_NONBONDED_DO_SHIFTFORCE;
 275         }
 276         if (flags & GMX_FORCE_ENERGY)
 277         {
 278             donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
 279         }
 280         if (flags & GMX_FORCE_DO_LR)
 281         {
 282             donb_flags |= GMX_NONBONDED_DO_LR;
 283         }
 284
 285         wallcycle_sub_start(wcycle, ewcsNONBONDED);
 286         do_nonbonded(fr, x, f, f_longrange, md, excl,
 287                      &enerd->grpp, nrnb,
 288                      lambda, dvdl_nb, -1, -1, donb_flags);
 289
 290         /* If we do foreign lambda and we have soft-core interactions
 291          * we have to recalculate the (non-linear) energies contributions.
 292          */
 293         if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) && fepvals->sc_alpha != 0)
 294         {
 295             for (i = 0; i < enerd->n_lambda; i++)
 296             {
 297                 for (j = 0; j < efptNR; j++)
 298                 {
 299                     lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
 300                 }
 301                 reset_foreign_enerdata(enerd);
 302                 do_nonbonded(fr, x, f, f_longrange, md, excl,
 303                              &(enerd->foreign_grpp), nrnb,
 304                              lam_i, dvdl_dum, -1, -1,
 305                              (donb_flags & ~GMX_NONBONDED_DO_FORCE) | GMX_NONBONDED_DO_FOREIGNLAMBDA);
 306                 sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
 307                 enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
 308             }
 309         }
 310         wallcycle_sub_stop(wcycle, ewcsNONBONDED);
 311         where();
 312     }
 313
 314     /* If we are doing GB, calculate bonded forces and apply corrections
 315      * to the solvation forces */
 316     /* MRS: Eventually, many need to include free energy contribution here! */
 317     if (ir->implicit_solvent)
 318     {
 319         wallcycle_sub_start(wcycle, ewcsBONDED);
 320         calc_gb_forces(cr, md, born, top, x, f, fr, idef,
 321                        ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
 322         wallcycle_sub_stop(wcycle, ewcsBONDED);
 323     }
 324
 325 #ifdef GMX_MPI
 326     if (TAKETIME)
 327     {
 328         t1          = MPI_Wtime();
 329         fr->t_fnbf += t1-t0;
 330     }
 331 #endif
 332
 333     if (fepvals->sc_alpha != 0)
 334     {
 335         enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
 336     }
 337     else
 338     {
 339         enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
 340     }
 341
 342     if (fepvals->sc_alpha != 0)
 343
 344     /* even though coulomb part is linear, we already added it, beacuse we
 345        need to go through the vdw calculation anyway */
 346     {
 347         enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
 348     }
 349     else
 350     {
 351         enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
 352     }
 353
 354     if (bSepDVDL)
 355     {
 356         real V_short_range    = 0;
 357         real dvdl_short_range = 0;
 358
 359         for (i = 0; i < enerd->grpp.nener; i++)
 360         {
 361             V_short_range +=
 362                 (fr->bBHAM ?
 363                  enerd->grpp.ener[egBHAMSR][i] :
 364                  enerd->grpp.ener[egLJSR][i])
 365                 + enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
 366         }
 367         dvdl_short_range = dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
 368         PRINT_SEPDVDL("VdW and Coulomb SR particle-p.",
 369                       V_short_range,
 370                       dvdl_short_range);
 371     }
 372     debug_gmx();
 373
 374
 375     if (debug)
 376     {
 377         pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
 378     }
 379
 380     /* Shift the coordinates. Must be done before bonded forces and PPPM,
 381      * but is also necessary for SHAKE and update, therefore it can NOT
 382      * go when no bonded forces have to be evaluated.
 383      */
 384
 385     /* Here sometimes we would not need to shift with NBFonly,
 386      * but we do so anyhow for consistency of the returned coordinates.
 387      */
 388     if (graph)
 389     {
 390         shift_self(graph, box, x);
 391         if (TRICLINIC(box))
 392         {
 393             inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
 394         }
 395         else
 396         {
 397             inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
 398         }
 399     }
 400     /* Check whether we need to do bondeds or correct for exclusions */
 401     if (fr->bMolPBC &&
 402         ((flags & GMX_FORCE_BONDED)
 403          || EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype)))
 404     {
 405         /* Since all atoms are in the rectangular or triclinic unit-cell,
 406          * only single box vector shifts (2 in x) are required.
 407          */
 408         set_pbc_dd(&pbc, fr->ePBC, cr->dd, TRUE, box);
 409     }
 410     debug_gmx();
 411
 412     if (flags & GMX_FORCE_BONDED)
 413     {
 414         wallcycle_sub_start(wcycle, ewcsBONDED);
 415         calc_bonds(fplog, cr->ms,
 416                    idef, x, hist, f, fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
 417                    DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL, atype, born,
 418                    flags,
 419                    fr->bSepDVDL && do_per_step(step, ir->nstlog), step);
 420
 421         /* Check if we have to determine energy differences
 422          * at foreign lambda's.
 423          */
 424         if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) &&
 425             idef->ilsort != ilsortNO_FE)
 426         {
 427             if (idef->ilsort != ilsortFE_SORTED)
 428             {
 429                 gmx_incons("The bonded interactions are not sorted for free energy");
 430             }
 431             for (i = 0; i < enerd->n_lambda; i++)
 432             {
 433                 reset_foreign_enerdata(enerd);
 434                 for (j = 0; j < efptNR; j++)
 435                 {
 436                     lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
 437                 }
 438                 calc_bonds_lambda(fplog, idef, x, fr, &pbc, graph, &(enerd->foreign_grpp), enerd->foreign_term, nrnb, lam_i, md,
 439                                   fcd, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
 440                 sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
 441                 enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
 442             }
 443         }
 444         debug_gmx();
 445
 446         wallcycle_sub_stop(wcycle, ewcsBONDED);
 447     }
 448
 449     where();
 450
 451     *cycles_pme = 0;
 452     clear_mat(fr->vir_el_recip);
 453     clear_mat(fr->vir_lj_recip);
 454
 455     /* Do long-range electrostatics and/or LJ-PME, including related short-range
 456      * corrections.
 457      */
 458     if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
 459     {
 460         real Vlr               = 0, Vcorr = 0;
 461         real dvdl_long_range   = 0;
 462         int  status            = 0;
 463         real Vlr_q             = 0, Vlr_lj = 0, Vcorr_q = 0, Vcorr_lj = 0;
 464         real dvdl_long_range_q = 0, dvdl_long_range_lj = 0;
 465
 466         bSB = (ir->nwall == 2);
 467         if (bSB)
 468         {
 469             copy_mat(box, boxs);
 470             svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
 471             box_size[ZZ] *= ir->wall_ewald_zfac;
 472         }
 473
 474         if (EEL_PME_EWALD(fr->eeltype) || EVDW_PME(fr->vdwtype))
 475         {
 476             real dvdl_long_range_correction_q   = 0;
 477             real dvdl_long_range_correction_lj  = 0;
 478             /* With the Verlet scheme exclusion forces are calculated
 479              * in the non-bonded kernel.
 480              */
 481             /* The TPI molecule does not have exclusions with the rest
 482              * of the system and no intra-molecular PME grid
 483              * contributions will be calculated in
 484              * gmx_pme_calc_energy.
 485              */
 486             if ((ir->cutoff_scheme == ecutsGROUP && fr->n_tpi == 0) ||
 487                 ir->ewald_geometry != eewg3D ||
 488                 ir->epsilon_surface != 0)
 489             {
 490                 int nthreads, t;
 491
 492                 wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
 493
 494                 if (fr->n_tpi > 0)
 495                 {
 496                     gmx_fatal(FARGS, "TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
 497                 }
 498
 499                 nthreads = gmx_omp_nthreads_get(emntBonded);
 500 #pragma omp parallel for num_threads(nthreads) schedule(static)
 501                 for (t = 0; t < nthreads; t++)
 502                 {
 503                     int     s, e, i;
 504                     rvec   *fnv;
 505                     tensor *vir_q, *vir_lj;
 506                     real   *Vcorrt_q, *Vcorrt_lj, *dvdlt_q, *dvdlt_lj;
 507                     if (t == 0)
 508                     {
 509                         fnv       = fr->f_novirsum;
 510                         vir_q     = &fr->vir_el_recip;
 511                         vir_lj    = &fr->vir_lj_recip;
 512                         Vcorrt_q  = &Vcorr_q;
 513                         Vcorrt_lj = &Vcorr_lj;
 514                         dvdlt_q   = &dvdl_long_range_correction_q;
 515                         dvdlt_lj  = &dvdl_long_range_correction_lj;
 516                     }
 517                     else
 518                     {
 519                         fnv       = fr->f_t[t].f;
 520                         vir_q     = &fr->f_t[t].vir_q;
 521                         vir_lj    = &fr->f_t[t].vir_lj;
 522                         Vcorrt_q  = &fr->f_t[t].Vcorr_q;
 523                         Vcorrt_lj = &fr->f_t[t].Vcorr_lj;
 524                         dvdlt_q   = &fr->f_t[t].dvdl[efptCOUL];
 525                         dvdlt_lj  = &fr->f_t[t].dvdl[efptVDW];
 526                         for (i = 0; i < fr->natoms_force; i++)
 527                         {
 528                             clear_rvec(fnv[i]);
 529                         }
 530                         clear_mat(*vir_q);
 531                         clear_mat(*vir_lj);
 532                     }
 533                     *dvdlt_q  = 0;
 534                     *dvdlt_lj = 0;
 535
 536                     ewald_LRcorrection(fr->excl_load[t], fr->excl_load[t+1],
 537                                        cr, t, fr,
 538                                        md->chargeA,
 539                                        md->nChargePerturbed ? md->chargeB : NULL,
 540                                        md->sqrt_c6A,
 541                                        md->nTypePerturbed ? md->sqrt_c6B : NULL,
 542                                        md->sigmaA,
 543                                        md->nTypePerturbed ? md->sigmaB : NULL,
 544                                        md->sigma3A,
 545                                        md->nTypePerturbed ? md->sigma3B : NULL,
 546                                        ir->cutoff_scheme != ecutsVERLET,
 547                                        excl, x, bSB ? boxs : box, mu_tot,
 548                                        ir->ewald_geometry,
 549                                        ir->epsilon_surface,
 550                                        fnv, *vir_q, *vir_lj,
 551                                        Vcorrt_q, Vcorrt_lj,
 552                                        lambda[efptCOUL], lambda[efptVDW],
 553                                        dvdlt_q, dvdlt_lj);
 554                 }
 555                 if (nthreads > 1)
 556                 {
 557                     reduce_thread_forces(fr->natoms_force, fr->f_novirsum,
 558                                          fr->vir_el_recip, fr->vir_lj_recip,
 559                                          &Vcorr_q, &Vcorr_lj,
 560                                          &dvdl_long_range_correction_q,
 561                                          &dvdl_long_range_correction_lj,
 562                                          nthreads, fr->f_t);
 563                 }
 564                 wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
 565             }
 566
 567             if (EEL_PME_EWALD(fr->eeltype) && fr->n_tpi == 0)
 568             {
 569                 Vcorr_q += ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
 570                                                    &dvdl_long_range_correction_q,
 571                                                    fr->vir_el_recip);
 572             }
 573
 574             PRINT_SEPDVDL("Ewald excl./charge/dip. corr.", Vcorr_q, dvdl_long_range_correction_q);
 575             PRINT_SEPDVDL("Ewald excl. corr. LJ", Vcorr_lj, dvdl_long_range_correction_lj);
 576             enerd->dvdl_lin[efptCOUL] += dvdl_long_range_correction_q;
 577             enerd->dvdl_lin[efptVDW]  += dvdl_long_range_correction_lj;
 578
 579             if ((EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype)) && (cr->duty & DUTY_PME))
 580             {
 581                 /* Do reciprocal PME for Coulomb and/or LJ. */
 582                 assert(fr->n_tpi >= 0);
 583                 if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
 584                 {
 585                     pme_flags = GMX_PME_SPREAD | GMX_PME_SOLVE;
 586                     if (EEL_PME(fr->eeltype))
 587                     {
 588                         pme_flags     |= GMX_PME_DO_COULOMB;
 589                     }
 590                     if (EVDW_PME(fr->vdwtype))
 591                     {
 592                         pme_flags |= GMX_PME_DO_LJ;
 593                     }
 594                     if (flags & GMX_FORCE_FORCES)
 595                     {
 596                         pme_flags |= GMX_PME_CALC_F;
 597                     }
 598                     if (flags & GMX_FORCE_VIRIAL)
 599                     {
 600                         pme_flags |= GMX_PME_CALC_ENER_VIR;
 601                     }
 602                     if (fr->n_tpi > 0)
 603                     {
 604                         /* We don't calculate f, but we do want the potential */
 605                         pme_flags |= GMX_PME_CALC_POT;
 606                     }
 607                     wallcycle_start(wcycle, ewcPMEMESH);
 608                     status = gmx_pme_do(fr->pmedata,
 609                                         0, md->homenr - fr->n_tpi,
 610                                         x, fr->f_novirsum,
 611                                         md->chargeA, md->chargeB,
 612                                         md->sqrt_c6A, md->sqrt_c6B,
 613                                         md->sigmaA, md->sigmaB,
 614                                         bSB ? boxs : box, cr,
 615                                         DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
 616                                         DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
 617                                         nrnb, wcycle,
 618                                         fr->vir_el_recip, fr->ewaldcoeff_q,
 619                                         fr->vir_lj_recip, fr->ewaldcoeff_lj,
 620                                         &Vlr_q, &Vlr_lj,
 621                                         lambda[efptCOUL], lambda[efptVDW],
 622                                         &dvdl_long_range_q, &dvdl_long_range_lj, pme_flags);
 623                     *cycles_pme = wallcycle_stop(wcycle, ewcPMEMESH);
 624                     if (status != 0)
 625                     {
 626                         gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
 627                     }
 628                     /* We should try to do as little computation after
 629                      * this as possible, because parallel PME synchronizes
 630                      * the nodes, so we want all load imbalance of the
 631                      * rest of the force calculation to be before the PME
 632                      * call.  DD load balancing is done on the whole time
 633                      * of the force call (without PME).
 634                      */
 635                 }
 636                 if (fr->n_tpi > 0)
 637                 {
 638                     if (EVDW_PME(ir->vdwtype))
 639                     {
 640
 641                         gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
 642                     }
 643                     /* Determine the PME grid energy of the test molecule
 644                      * with the PME grid potential of the other charges.
 645                      */
 646                     gmx_pme_calc_energy(fr->pmedata, fr->n_tpi,
 647                                         x + md->homenr - fr->n_tpi,
 648                                         md->chargeA + md->homenr - fr->n_tpi,
 649                                         &Vlr_q);
 650                 }
 651                 PRINT_SEPDVDL("PME mesh", Vlr_q + Vlr_lj, dvdl_long_range_q+dvdl_long_range_lj);
 652             }
 653         }
 654
 655         if (!EEL_PME(fr->eeltype) && EEL_PME_EWALD(fr->eeltype))
 656         {
 657             Vlr_q = do_ewald(ir, x, fr->f_novirsum,
 658                              md->chargeA, md->chargeB,
 659                              box_size, cr, md->homenr,
 660                              fr->vir_el_recip, fr->ewaldcoeff_q,
 661                              lambda[efptCOUL], &dvdl_long_range_q, fr->ewald_table);
 662             PRINT_SEPDVDL("Ewald long-range", Vlr_q, dvdl_long_range_q);
 663         }
 664
 665         /* Note that with separate PME nodes we get the real energies later */
 666         enerd->dvdl_lin[efptCOUL] += dvdl_long_range_q;
 667         enerd->dvdl_lin[efptVDW]  += dvdl_long_range_lj;
 668         enerd->term[F_COUL_RECIP]  = Vlr_q + Vcorr_q;
 669         enerd->term[F_LJ_RECIP]    = Vlr_lj + Vcorr_lj;
 670         if (debug)
 671         {
 672             fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
 673                     Vlr_q, Vcorr_q, enerd->term[F_COUL_RECIP]);
 674             pr_rvecs(debug, 0, "vir_el_recip after corr", fr->vir_el_recip, DIM);
 675             pr_rvecs(debug, 0, "fshift after LR Corrections", fr->fshift, SHIFTS);
 676             fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n",
 677                     Vlr_lj, Vcorr_lj, enerd->term[F_LJ_RECIP]);
 678             pr_rvecs(debug, 0, "vir_lj_recip after corr", fr->vir_lj_recip, DIM);
 679         }
 680     }
 681     else
 682     {
 683         /* Is there a reaction-field exclusion correction needed? */
 684         if (EEL_RF(fr->eeltype) && eelRF_NEC != fr->eeltype)
 685         {
 686             /* With the Verlet scheme, exclusion forces are calculated
 687              * in the non-bonded kernel.
 688              */
 689             if (ir->cutoff_scheme != ecutsVERLET)
 690             {
 691                 real dvdl_rf_excl      = 0;
 692                 enerd->term[F_RF_EXCL] =
 693                     RF_excl_correction(fr, graph, md, excl, x, f,
 694                                        fr->fshift, &pbc, lambda[efptCOUL], &dvdl_rf_excl);
 695
 696                 enerd->dvdl_lin[efptCOUL] += dvdl_rf_excl;
 697                 PRINT_SEPDVDL("RF exclusion correction",
 698                               enerd->term[F_RF_EXCL], dvdl_rf_excl);
 699             }
 700         }
 701     }
 702     where();
 703     debug_gmx();
 704
 705     if (debug)
 706     {
 707         print_nrnb(debug, nrnb);
 708     }
 709     debug_gmx();
 710
 711 #ifdef GMX_MPI
 712     if (TAKETIME)
 713     {
 714         t2 = MPI_Wtime();
 715         MPI_Barrier(cr->mpi_comm_mygroup);
 716         t3          = MPI_Wtime();
 717         fr->t_wait += t3-t2;
 718         if (fr->timesteps == 11)
 719         {
 720             fprintf(stderr, "* PP load balancing info: node %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
 721                     cr->nodeid, gmx_step_str(fr->timesteps, buf),
 722                     100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
 723                     (fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
 724         }
 725         fr->timesteps++;
 726     }
 727 #endif
 728
 729     if (debug)
 730     {
 731         pr_rvecs(debug, 0, "fshift after bondeds", fr->fshift, SHIFTS);
 732     }
 733
 734 }
 735
 736 void init_enerdata(int ngener, int n_lambda, gmx_enerdata_t *enerd)
 737 {
 738     int i, n2;
 739
 740     for (i = 0; i < F_NRE; i++)
 741     {
 742         enerd->term[i]         = 0;
 743         enerd->foreign_term[i] = 0;
 744     }
 745
 746
 747     for (i = 0; i < efptNR; i++)
 748     {
 749         enerd->dvdl_lin[i]     = 0;
 750         enerd->dvdl_nonlin[i]  = 0;
 751     }
 752
 753     n2 = ngener*ngener;
 754     if (debug)
 755     {
 756         fprintf(debug, "Creating %d sized group matrix for energies\n", n2);
 757     }
 758     enerd->grpp.nener         = n2;
 759     enerd->foreign_grpp.nener = n2;
 760     for (i = 0; (i < egNR); i++)
 761     {
 762         snew(enerd->grpp.ener[i], n2);
 763         snew(enerd->foreign_grpp.ener[i], n2);
 764     }
 765
 766     if (n_lambda)
 767     {
 768         enerd->n_lambda = 1 + n_lambda;
 769         snew(enerd->enerpart_lambda, enerd->n_lambda);
 770     }
 771     else
 772     {
 773         enerd->n_lambda = 0;
 774     }
 775 }
 776
 777 void destroy_enerdata(gmx_enerdata_t *enerd)
 778 {
 779     int i;
 780
 781     for (i = 0; (i < egNR); i++)
 782     {
 783         sfree(enerd->grpp.ener[i]);
 784     }
 785
 786     for (i = 0; (i < egNR); i++)
 787     {
 788         sfree(enerd->foreign_grpp.ener[i]);
 789     }
 790
 791     if (enerd->n_lambda)
 792     {
 793         sfree(enerd->enerpart_lambda);
 794     }
 795 }
 796
 797 static real sum_v(int n, real v[])
 798 {
 799     real t;
 800     int  i;
 801
 802     t = 0.0;
 803     for (i = 0; (i < n); i++)
 804     {
 805         t = t + v[i];
 806     }
 807
 808     return t;
 809 }
 810
 811 void sum_epot(gmx_grppairener_t *grpp, real *epot)
 812 {
 813     int i;
 814
 815     /* Accumulate energies */
 816     epot[F_COUL_SR]  = sum_v(grpp->nener, grpp->ener[egCOULSR]);
 817     epot[F_LJ]       = sum_v(grpp->nener, grpp->ener[egLJSR]);
 818     epot[F_LJ14]     = sum_v(grpp->nener, grpp->ener[egLJ14]);
 819     epot[F_COUL14]   = sum_v(grpp->nener, grpp->ener[egCOUL14]);
 820     epot[F_COUL_LR]  = sum_v(grpp->nener, grpp->ener[egCOULLR]);
 821     epot[F_LJ_LR]    = sum_v(grpp->nener, grpp->ener[egLJLR]);
 822     /* We have already added 1-2,1-3, and 1-4 terms to F_GBPOL */
 823     epot[F_GBPOL]   += sum_v(grpp->nener, grpp->ener[egGB]);
 824
 825 /* lattice part of LR doesnt belong to any group
 826  * and has been added earlier
 827  */
 828     epot[F_BHAM]     = sum_v(grpp->nener, grpp->ener[egBHAMSR]);
 829     epot[F_BHAM_LR]  = sum_v(grpp->nener, grpp->ener[egBHAMLR]);
 830
 831     epot[F_EPOT] = 0;
 832     for (i = 0; (i < F_EPOT); i++)
 833     {
 834         if (i != F_DISRESVIOL && i != F_ORIRESDEV)
 835         {
 836             epot[F_EPOT] += epot[i];
 837         }
 838     }
 839 }
 840
 841 void sum_dhdl(gmx_enerdata_t *enerd, real *lambda, t_lambda *fepvals)
 842 {
 843     int    i, j, index;
 844     double dlam;
 845
 846     enerd->dvdl_lin[efptVDW] += enerd->term[F_DVDL_VDW];  /* include dispersion correction */
 847     enerd->term[F_DVDL]       = 0.0;
 848     for (i = 0; i < efptNR; i++)
 849     {
 850         if (fepvals->separate_dvdl[i])
 851         {
 852             /* could this be done more readably/compactly? */
 853             switch (i)
 854             {
 855                 case (efptMASS):
 856                     index = F_DKDL;
 857                     break;
 858                 case (efptCOUL):
 859                     index = F_DVDL_COUL;
 860                     break;
 861                 case (efptVDW):
 862                     index = F_DVDL_VDW;
 863                     break;
 864                 case (efptBONDED):
 865                     index = F_DVDL_BONDED;
 866                     break;
 867                 case (efptRESTRAINT):
 868                     index = F_DVDL_RESTRAINT;
 869                     break;
 870                 default:
 871                     index = F_DVDL;
 872                     break;
 873             }
 874             enerd->term[index] = enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
 875             if (debug)
 876             {
 877                 fprintf(debug, "dvdl-%s[%2d]: %f: non-linear %f + linear %f\n",
 878                         efpt_names[i], i, enerd->term[index], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
 879             }
 880         }
 881         else
 882         {
 883             enerd->term[F_DVDL] += enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
 884             if (debug)
 885             {
 886                 fprintf(debug, "dvd-%sl[%2d]: %f: non-linear %f + linear %f\n",
 887                         efpt_names[0], i, enerd->term[F_DVDL], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
 888             }
 889         }
 890     }
 891
 892     /* Notes on the foreign lambda free energy difference evaluation:
 893      * Adding the potential and ekin terms that depend linearly on lambda
 894      * as delta lam * dvdl to the energy differences is exact.
 895      * For the constraints this is not exact, but we have no other option
 896      * without literally changing the lengths and reevaluating the energies at each step.
 897      * (try to remedy this post 4.6 - MRS)
 898      * For the non-bonded LR term we assume that the soft-core (if present)
 899      * no longer affects the energy beyond the short-range cut-off,
 900      * which is a very good approximation (except for exotic settings).
 901      * (investigate how to overcome this post 4.6 - MRS)
 902      */
 903     if (fepvals->separate_dvdl[efptBONDED])
 904     {
 905         enerd->term[F_DVDL_BONDED] += enerd->term[F_DVDL_CONSTR];
 906     }
 907     else
 908     {
 909         enerd->term[F_DVDL] += enerd->term[F_DVDL_CONSTR];
 910     }
 911     enerd->term[F_DVDL_CONSTR] = 0;
 912
 913     for (i = 0; i < fepvals->n_lambda; i++)
 914     {
 915         /* note we are iterating over fepvals here!
 916            For the current lam, dlam = 0 automatically,
 917            so we don't need to add anything to the
 918            enerd->enerpart_lambda[0] */
 919
 920         /* we don't need to worry about dvdl_lin contributions to dE at
 921            current lambda, because the contributions to the current
 922            lambda are automatically zeroed */
 923
 924         for (j = 0; j < efptNR; j++)
 925         {
 926             /* Note that this loop is over all dhdl components, not just the separated ones */
 927             dlam = (fepvals->all_lambda[j][i]-lambda[j]);
 928             enerd->enerpart_lambda[i+1] += dlam*enerd->dvdl_lin[j];
 929             if (debug)
 930             {
 931                 fprintf(debug, "enerdiff lam %g: (%15s), non-linear %f linear %f*%f\n",
 932                         fepvals->all_lambda[j][i], efpt_names[j],
 933                         (enerd->enerpart_lambda[i+1] - enerd->enerpart_lambda[0]),
 934                         dlam, enerd->dvdl_lin[j]);
 935             }
 936         }
 937     }
 938 }
 939
 940
 941 void reset_foreign_enerdata(gmx_enerdata_t *enerd)
 942 {
 943     int  i, j;
 944
 945     /* First reset all foreign energy components.  Foreign energies always called on
 946        neighbor search steps */
 947     for (i = 0; (i < egNR); i++)
 948     {
 949         for (j = 0; (j < enerd->grpp.nener); j++)
 950         {
 951             enerd->foreign_grpp.ener[i][j] = 0.0;
 952         }
 953     }
 954
 955     /* potential energy components */
 956     for (i = 0; (i <= F_EPOT); i++)
 957     {
 958         enerd->foreign_term[i] = 0.0;
 959     }
 960 }
 961
 962 void reset_enerdata(t_forcerec *fr, gmx_bool bNS,
 963                     gmx_enerdata_t *enerd,
 964                     gmx_bool bMaster)
 965 {
 966     gmx_bool bKeepLR;
 967     int      i, j;
 968
 969     /* First reset all energy components, except for the long range terms
 970      * on the master at non neighbor search steps, since the long range
 971      * terms have already been summed at the last neighbor search step.
 972      */
 973     bKeepLR = (fr->bTwinRange && !bNS);
 974     for (i = 0; (i < egNR); i++)
 975     {
 976         if (!(bKeepLR && bMaster && (i == egCOULLR || i == egLJLR)))
 977         {
 978             for (j = 0; (j < enerd->grpp.nener); j++)
 979             {
 980                 enerd->grpp.ener[i][j] = 0.0;
 981             }
 982         }
 983     }
 984     for (i = 0; i < efptNR; i++)
 985     {
 986         enerd->dvdl_lin[i]    = 0.0;
 987         enerd->dvdl_nonlin[i] = 0.0;
 988     }
 989
 990     /* Normal potential energy components */
 991     for (i = 0; (i <= F_EPOT); i++)
 992     {
 993         enerd->term[i] = 0.0;
 994     }
 995     /* Initialize the dVdlambda term with the long range contribution */
 996     /* Initialize the dvdl term with the long range contribution */
 997     enerd->term[F_DVDL]            = 0.0;
 998     enerd->term[F_DVDL_COUL]       = 0.0;
 999     enerd->term[F_DVDL_VDW]        = 0.0;
1000     enerd->term[F_DVDL_BONDED]     = 0.0;
1001     enerd->term[F_DVDL_RESTRAINT]  = 0.0;
1002     enerd->term[F_DKDL]            = 0.0;
1003     if (enerd->n_lambda > 0)
1004     {
1005         for (i = 0; i < enerd->n_lambda; i++)
1006         {
1007             enerd->enerpart_lambda[i] = 0.0;
1008         }
1009     }
1010     /* reset foreign energy data - separate function since we also call it elsewhere */
1011     reset_foreign_enerdata(enerd);
1012 }